Sunday, August 30, 2015

PhyloPic

A few weeks ago we discussed a paper in our journal club that used dinosaur silhouettes in its figures and referenced PhyloPic as the source. So today I finally decided to check the website out.

PhyloPic is a repository of black/white silhouettes of organisms across the tree of life. The idea is that everybody can sign up and submit their artwork under some kind of creative commons or public domain license, and everybody can use the silhouettes to do just what the authors in the aforementioned paper did: decorate phylogenetic tree figures in publications or talk slides, educate, etc.

The idea sounds great, so I played around a bit today to see how well it works. The experience was, alas, a bit mixed.

Saturday, August 29, 2015

Comment moderation on

Some spam bot seems to have discovered this blog, and it is getting annoying. Consequently I have just turned comment moderation on. I don't think it will make a lot of difference to readers of this blog. Discussions or questions happen, but they are rare.

Most people seem to find my blog when googling for one of the topics I have covered, especially phylogenetic systematics, the aromatic plant genus Minthostachys, the various posts on how to use this or that software tool or method, and, somewhat more to my surprise, three very specific posts on acknowledging peer reviewers, ResearchGate, and bracketed versus indented keys.

And that was always the idea: I don't expect to host any long discussions about paraphyletic taxa here, but maybe somebody will find some of my perspectives, information and how-to's useful. Comment moderation won't interfere with that, but it will make sure all those gibberish comments ending with links to health supplement sellers won't get through, and that's a plus.

Friday, August 28, 2015

Botany picture #212: Pachystachys spicata


At the moment I can't find the energy to write anything substantial, but I can just fill the blog with plant pictures that I have taken over the years. Here is another pretty Acanthaceae - a family that I have quite a lot of photographs of. Pachystachys spicata, originally from northern Bolivia, but in this case photographed at the Botanic Garden of Goettingen University. It is a weak-stemmed, scraggly shrub, and the flowers are obviously meant for hummingbird pollination.

Yellow-white Pachystachys lutea is more widely known and more often seen in botanic gardens, but I like the above species better.

Sunday, August 23, 2015

Andere Laender, andere Sitten

One thing that gave me a bit of a culture shock after coming to Australia was the way in which plant taxonomists work here compared to how I had been trained by European and North and South American taxonomists.

Sunday, August 16, 2015

Cracked explains what is wrong with science - or tries to

Sometimes I really wish people who try to write very confidently about a subject would at least make a token effort at trying to research the topic first. Or, failing that, perhaps because they don't have the time, at least try not to sound so damn Dunning-Kruger about it.

The listicle website Cracked recently tried to explain why science is broken, in six bullet points (hat tip: RationalWiki):

6. Publication bias towards positive results.

5. Scientists not having to make the data underlying their studies available.

4. Scientists having to pay publication fees, which creates perverse incentives and restricts access to publication venues for scientists from poorer countries.

3. Big publishing companies earning obscene profits by charging journal subscription fees in addition to publication fees, thereby restricting access to the results of research.

2. Scientists being forbidden from giving out reprints of their papers because they signed over the copyright to aforementioned publishers.

1. Predatory journals publishing nonsense science.

Except for the first point (#6), all of this is either misleading or self-contradictory.

Friday, August 14, 2015

Botany picture(s) #211: Macrozamia communis

So, about this cycad I mentioned the other day. When I was a student in Germany, cycads were these really weird plants form the dinosaur age of which you may see one or two in the greenhouses of the botanic gardens. Exotic, rare, spectacular.

Here in Australia, I drive an hour and a half to the east where it gets a bit wetter and milder, and the whole forest floor is covered in them.

But yes, they were more diverse and abundant during the Mesozoic, and they appear to be a bit odd just because there are so few of them left. Essentially they look like a cross between a palm and a conifer: on the one hand they have large, pinnate leaves and fat, un- or rarely branched stems, on the other hand they are gymnosperms, carrying their ovules and thus their seeds freely on the surface of specialised leaves that are generally arranged in cones.


The above is a male cone of Macrozamia communis. I placed it on the dirt road for photographing because there was little light in the understorey.


The individual microsporophylls - the male leaf organs that are homologous to stamens in flowering plants - have large numbers of scattered pollen sacs. A far cry from the regularly four pollen sacs on the familiar, small angiosperm stamens.



I had seen and photographed male cones before, but our little stroke of luck on the recent field trip was to come across a mature female cone so that we could discuss it with the students. The megasporophylls have a long petiole, a spine at the end, and two ovules. Pollination success seems to be extremely high.

I have not observed it myself, but I am being told that these plants are actually insect pollinated. Apparently they warm up their cones in the evening and attract large numbers of beetles that spend the night there.


The outer coat of the seeds is kind of plasticy-spongy and orange-red, indicating that it is probably meant to be eaten to disperse the seeds. However, according to ANU professor Mike Crisp there is no native animal that does eat them; it is possible that the dispersing agent was part of the extinct macrofauna of the continent.

That being said, one of my colleagues mentioned over lunch that feral pigs supposedly eat them. If that is the case, and if the seeds come out undamaged, the plant may have found a new dispersing agent.

Wednesday, August 12, 2015

Students using dichotomous keys and a Lucid multi-access key

Today I and a colleague from the ANU supervised a group of students while they tried to identify seven species of Acacia (Fabaceae) using different types of keys. On offer were the book version of the Flora of New South Wales with its traditional dichotomous key, the online version of the same flora using pretty much the same dichotomous key, and the Lucid based Wattle Key, which is multi-entry.

I have written about dichotomous versus multi-entry keys before. The purpose of today's course was three-fold: to learn something about Acacia, as it is a very important and iconic part of the Australian flora, to become confident at using identification keys, but also to form a personal opinion on which type of key one would be more comfortable with. In other words, I encouraged the students to try both variants. I found the travails of some of them most informative, even more so than last year when we did the same course (perhaps because then I was more busy - the course was then twice as large).

A few observations: